pyrI:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10811 ECOCYC:EG10811]
EcoCyc:EG10811
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10811 EcoGene:EG10811]
EcoGene:EG10811
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120000802
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB0804
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0013889
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:35, 27 May 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

pyrI

Mnemonic

Pyrimidine

Synonyms

ECK4239, b4244, JW4203[1], JW4203

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

96.32 minutes, 96.32 minutes 

MG1655: 4469470..4469009
<gbrowseImage> name=NC_000913:4469009..4469470 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4454724..4454263
<gbrowseImage> name=NC_012967:4454263..4454724 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4407744..4408205
<gbrowseImage> name=NC_012759:4407744..4408205 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4476127..4475666
<gbrowseImage> name=AC_000091:4475666..4476127 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4571278..4570817
<gbrowseImage> name=NC_010473:4570817..4571278 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

4469012

Edman degradation

PMID:4872216[2]
PMID:8740179[3]
PMID:9298646[4]


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔpyrI (Keio:JW4203)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC11025[6]

ΔpyrI720::kan

PMID:16738554[5]

CGSC:102576


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW4203

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACACACGATAATAAATTGCA

Primer 2:CCATTGGCCAGCACCACATTATG

E1F5

Kohara Phage

Genobase

PMID:3038334[8]

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[6]

est. P1 cotransduction: 40% [9]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[6]

est. P1 cotransduction: % [9]
Synonyms:zjj-202::Tn10, zji-202::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10811

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10811

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948763

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000802

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0804

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013889

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Weber, K (1968) New structural model of E. coli aspartate transcarbamylase and the amino-acid sequence of the regulatory polypeptide chain. Nature 218 1116-9 PubMed
  3. ↑ Pasquali, C et al. (1996) Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 17 547-55 PubMed
  4. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  5. ↑ 5.0 5.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  8. ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  9. ↑ 9.0 9.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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